By authority granted by the Confiscation Acts of 1861 and 1862, the constitutionality of which was upheld by the Supreme Court in the Prize Cases (67 US 635)decision issued in 1863. Under the Confiscation Acts, the federal government could seize any private property without compensation if it was being used to further the cause of the Southern rebellion. Since Northern states were not in rebellion the law did not apply to them.
Right, nor was that in the 1860 Republican party platform.
What Congress then could do, but Fire Eaters denied, was abolish slavery in US territories, and that's what the Republican platform did call for.
It was enough to drive Southern Democrats insane with rage and secession declarations.
Svartalfiar: "Yet, according to him/all of y'all, the South's secessions weren't legal, and those states never truly left the Union."
Of course, since neither condition our Founders acknowledged as valid for disunion existed in 1860: 1) necessity and 2) mutual consent.
Svartalfiar: "So by what authority could he then free slaves in those states, but not the northern ones?"
The term they used was "contraband of war" meaning a President as commander in chief could declare certain enemy properties "contraband" and seize it without compensating its owners.
It was by no means a new idea, had been around for centuries.
Svartalfiar: "You can't have it both ways - either 1). the South truly left and had to be beaten back in, in which case he had no power or authority over the Confederacy to issue his Proclamation, or 2). the states were always in the Union and he couldn't have freed the Southern slaves yet had no power to free those in the North."
I think you probably know the real answer already.
Do you remember that the Confederacy issued a formal declaration of war against the United States on May 6, 1861?
That should eliminate any doubts as to the status of Confederate officials, regardless of whether they were considered legitimate or not -- they were, by their own declaration of war, enemies of the United States and therefore subject to normal wartime treatment.
As such their property could be declared "contraband of war" and seized by the Federal government.
That contraband rule applied regardless of which of the two conditions you posited above was in effect.
By sharp contrast: so long as Southern Union states did not join the rebellion, they must be treated according to Constitutional requirements.
How is that not clear?